PSOM Research Core Facilities - Perelman School of ......Advertising brochure in process Central Core Director Guide open Central Discuss Penn Genomics Strucure open Central Collect

PSOM Research Core Facilities

Lou Soslowsky, PhD Associate Dean for Research Core Facilities

Outline • People and Cores • Recent Activities • Brief Summary of Each Core • Core Project Examples • Areas of Focus Going Forward

Outline • People and Cores • Recent Activities • Brief Summary of Each Core • Core Project Examples • Areas of Focus Going Forward

Cores Committee

Lou Soslowsky, Orthopaedic Surgery Michael Beers, Medicine Michael Betts, Microbiology Maja Bucan, Genetics Yale Goldman, Physiology Warren Pear, Pathology Celeste Simon, CDB Nancy Speck, CDB Admin Support: Jenna Ruttkay & Jenna Roberg

Perelman School of Medicine CHOP

Harry Ischiropoulos

Wistar

Bill Wunner

Ex Officio

Jiju Mathew, Finance Susan Passante, EVD/CSO Danielle Rehr, Finance Brian Wells, IT & Research Computing

First Year Activities Area REQUESTS / TO DO Status

Advertising website: update everyone's keywords open Advertising brochure in process Central Core Director Guide open Central Discuss Penn Genomics Strucure open Central Collect FY16 annual reports from Cores in process Central review FY16 core requests/cost open Central invite cores to present at committee meetings open Central support faculty recruiting ongoing Central Cores Statistics for PSOM use on hold Central educational opportunity via Dan Kessler on hold Central Business Plan for Centralization in process - J. Mathew Central iLab - determine fiscal/admin plan for BA roles in process - J. Mathew Central Penn CRISPR Cas 9 Targeting Core in process Central High-Throughput Screening Growth in process Central 11/17 Cores Presentation in process Central Winter 2016 Cores Newsletter in process Central Mission Continuity in process Central Cores Survey Email to PSOM in process Central Cores Survey Updates in process

Central Recruit Committee Member to replace Y. Goldman starting Jan 17 open

Finance obtain updated 5yr fiscal report from Finance in process Meetings Agenda for 10/28 Cores Committee Meeting in process Advertising Fall Cores newsletter complete Cores Fair 2016 Cores Fair complete Central request FY16 annual reports complete Advertising website - add grant proposal language complete Advertising communicate opportunity for individual core videos complete Cores Fair determing 2016 Cores Fair location and options complete Central annual report responses complete Central S10 communication process complete Cores Fair determine 2016 Cores Fair date complete Cores Fair determine 2016 Cores Fair date complete Advertising website: welcome video complete Advertising Website - transition to MODX complete Advertising Website - add S10 request complete Central Penn Box folder for Cores documents complete Central SCDC meeting per Tom Hecker complete Central announce new proteomics core complete Central Core Community Faculty Meetings complete Central Collect annual reports from Cores complete Central Record Welcome Video from Lou complete Central review FY16 core requests/cost complete Advertising Website - add user survey complete Central PGT - determine go-forward strategy complete

Central iLab - determine line of roles/responsibilities between iLab and CAMS complete

Central Make Directory and Map for Cores Fair complete Central Hold 2015 Cores Fair Directors Meeting complete Central 2015 Cores Fair complete Central Design ad for NERLSCD pamphlet complete Central Sponsor NERLSCD meeting complete Central Invite new members to Committee complete Advertising website: Associated Cores search bar closed Central Hold luncheon for Core Committee Members complete Central Meet with Core Directors complete Central Visit Wistar cores complete Central Visit each PSOM core location complete Advertising update EVD website re: cores information complete Advertising website: hover blurbs complete Advertising Website - add core committee members complete Central CHOP member transition complete Central review NGSC request complete Central update policies complete Central Ben Garcia: decision on stipend complete Central look into S10 process w/ VPR; determine go-forward process complete Central determine future of Proteomics Core complete Central Welcome to Celeste Simon complete Finance New Proteomics MOU complete Finance review CCVPF equipment request complete Finance PMI - New Service Center request complete Finance HTS MOU complete Meetings presentation of new proteomics core to Committee complete Meetings agenda for 12/18 Committee meeting complete Meetings agenda for 9/22 Cores Directors meeting complete

Example Accomplishments • Enhanced and diversified cores committee • Site visits to each core • One-on-one meetings with each core director • One-on-one meetings with multiple chairs • Campus-wide Research Core Facilities Fair • MOUs for multiple cores • Close/develop cores (recent and ongoing) • Revamped and enhanced website • Annual reports/reviews

Outline • People and Cores • Recent Activities • Brief Summary of Each Core • Core Project Examples • Areas of Focus Going Forward

23 PSOM Resource Core Facilities Bioinformatics Core CDB Microscopy Core CRISPR Cas9 Mouse Targeting

Core Cell Center Services Facility Cell Center Stockroom Clinical Cell and Vaccine

Production Facility Clinical Research Computing Unit Electron Microscopy Flow Cytometry and Cell Sorting

Facility High Throughput Screening Human Immunology Core Investigational Drug Service

Neurobehavior Testing Core Next Generation Sequencing Core Penn Genomic Analysis Core

DNA Sequencing Facility Molecular Profiling Facility

Penn Gnotobiotic Mouse Facility Quantitative Proteomics

Resource Core Research Instrumentation Shop Small Animal Imaging Facility Stem Cell and Xenograft Core Transgenic and Chimeric Mouse

Facility Vector Core

What Our Cores Offer • State-of-the-art equipment • Cutting-edge technical expertise and training • Support and consultations for faculty and trainees • Opportunities for scientific collaboration • Interest groups, seminars, meetings

Bioinformatics Core

• Data analysis and consulting

• Pipelines to handle next-generation sequencing data analysis

• Support for grant applications

• Additional services: – Application Development – Database Development – Large Scale Biomedical Data

Management

“CDB” Microscopy Core

• Five confocal and three widefield light microscopes, a scanning electron microscope

• Computers/software for image processing and analysis

• Personalized assistance on all aspects of imaging – sample preparation – microscope training – Image processing and

analysis

Cell Center Services Facility

• Training/services in cell culture and associated procedures

• Large scale growth of hybridoma and other cell lines

• Preparation of specialized culture media, drosophila media, and reagents

• Additional services: – culture in Celline flask and

hollow fiber bioreactor – hybridoma production/screening – transfection of mammalian cells

Cell Center Stockroom

• Relationships with various suppliers of molecular biological research materials for bulk purchasing, negotiation of discounts and convenient delivery

• Over 1,400 products on-site for immediate delivery

• Special order from 24 bioreagent vendors with discounted pricing and overnight delivery

Clinical Cell & Vaccine Production Facility • Scientific, technical and

regulatory support for investigator initiated investigational new drug applications in cell and gene therapy in GMP facility

• Services include: – Washing and cryopreservation of

pheresis product – Activation and expansion of donor

or patient T lymphocytes – Transduction of activated T cells

with retroviral or lentiviral vector – Generation of immature or

mature dendritic cells

Clinical Research Computing Unit

• Provides expertise in all facets of research information management (biomedical, behavioral, clinical, translational), and by understanding the regulatory and cultural environments

• Services include: – project management – data management and research

technology specializing in clinical research informatics

– collaboration and research IT services

CRISPR Cas9 Mouse Targeting Core

• CRISPR/Cas9 technology reduces the time and cost required to generate genetically engineered mice.

• In partnership with the Transgenic and Chimeric Mouse Facility, the core offers a variety of services including: – targeting design – sgRNA preparation – Cas9 mRNA generation – DNA repair template preparation – microinjection – genotyping/screening for

targeted mice

Electron Microscopy Resource Laboratory

• High quality ultrastructure analysis by electron microscopy (EM)

• Experienced staff and state-of-the-art preparation and imaging equipment

• Full spectrum of both transmission EM and scanning EM services

Flow Cytometry and Cell Sorting Facility

• Comprehensive flow cytometry (NCI laboratory of exceptional merit)

• Array of instrumentation, education, consultation – from high-speed multicolor to

low-speed, large nozzle – cell analysis services (up to 20

parameters), from analog, tabletop analyzers to many-laser, many-color, high-speed, fully-digital instrumentation

– 6 cell sorters and 19 analytical instruments

– BSL3 suite (10 parameter)

High-throughput Screening Core • HTS screening to identify

genes or organic small molecule modulators of signaling pathways, cellular phenotypes, and protein function staff will educate: – assay development,

optimization, miniaturization, validation

– libraries of siRNA, shRNA, cDNA, and FDA approved/ FDA-like organic small molecules

– robotics infrastructure, including small screens of user defined libraries

Human Immunology Core

• Reagents/expertise/ consultations for study of immune function in humans

• Cell and tissue processing, generation of human blood cell products

• Cellular/molecular immune assays for early-phase trials

• Multicolor immuno-phenotyping, sequencing of T and B cell receptor genes, luminex, ELISPOTs, ELISA

Investigational Drug Service

• Research pharmacy – management of research

medications used in clinical drug trials

– oversight of medication use in drug trials conducted throughout Penn and affiliates

• Agents overseen include drugs, natural products, vitamins, biologics and gene therapy agents

Neurobehavior Testing Core

• Consultation on study design (tests, mouse strains/lines, numbers, control groups, breeding, regulatory issues)

• Facilities and services to phenotype behaviors in mice – running wheels, beam splitters,

EEG/EMG recording chambers, open field activity monitors and Rotarod, various mazes, light/dark chamber, passive/active avoidance chambers and hole poke arenas, object recognition tests

Next Generation Sequencing Core

• Library quality assessments, sequencing, and analysis including ChIP-seq, RNA-Seq, HITS-CLIP, miR-Seq, exome capture, and BIS-seq

• Advice on library preparation and limited library preparation services

• Two Illumina hiSeq2000s for large-scale sequencing and a MiSeq for sample evaluation or library testing

Penn Genomic Analysis Core: DNA Sequencing Facility

• Long read, automated Sanger sequencing with fast turnaround

• NGS on Ion Torrent Personal Genome Machine and Proton

• Genotyping and fragment analysis

• Molecular biologic services • Data analysis

Penn Genomic Analysis Core: Molecular Profiling Facility

• DNA (Sequenom assays, and Illumina GoldenGate)

• RNA profiling (Affymetrix GeneChips, Illumina BeadChips, custom multiplex, Fluidigm, Luminex and deep sequencing)

• Whole-genome assays (Affymetrix SNP GeneChip and Illumina Infinium)

• Consultations, training, experimental design

Penn Gnotobiotic Mouse Facility

• Centralized germ-free and gnotobiotic mouse services

• Several common strains of germ-free mice and re-derivation services

• Isolators for germ-free and gnotobiotic mice for experimental procedures

• Technical support for procedures

Quantitative Proteomics Resource Core

• High resolution mass spectrometry-based proteomics to characterize and quantify proteins from complex biological samples

• Services include: – protein identification – protein post-translational

modification analyses – global histone PTM analyses – global proteome and

phosphoproteome analyses – experiments for custom

proteomics analyses

Research Instrumentation Shop

• Offers machine shop services including – making new mechanical

parts – design assistance – packaging of

electronics/optics – repairs of basic lab

equipment

Small Animal Imaging Facility

• Comprehensive suite of imaging modalities for cells, tissues, and small animals including: MRI, MRS, optical imaging (bioluminescence and near IR), CT, PET, SPECT, and ultrasound

• Housing for mice and rats for longitudinal studies

• Ancillary facilities such as chemistry, radiochemistry, image analysis and tumor models

Stem Cell and Xenograft Core

• Integrates viable tissue bank of normal human hematopoietic cells and hematopoietic malignancies with a wide range of xenograft services

• Facilitates and promotes translational research involving viable primary human hematopoietic tissues through training or full-service

Transgenic & Chimeric Mouse Facility

• Produces transgenic founder, chimeric and genome-edited strains of mice carrying transgenes or "knockouts"

• Services include: – cytoplasmic RNA injection (for CRISPR technology) – ES cell injection into blastocysts – DNA pronuclear injection into

fertilized oocytes – Embryo/sperm

cryopreservation – in vitro fertilization – re-derivations of lines

Vector Core

• Resource for the use of vectors for gene transfer

• Vector technology for preclinical and other basic research applications

• Tools critical to the understanding of gene function and development of therapeutic vectors

Outline • People and Cores • Recent Activities • Brief Summary of Each Core • Core Project Examples • Areas of Focus Going Forward

Flow Cytometry & Cell Sorting Resource Laboratory

• Research Question: To better understand the basic biology of

disseminated breast cancer cells (DTCs) or circulating tumor cells (CTCs)

• Method: A novel application (the BD Biosciences FACS Focus) to identify and isolate these very rare cells in patients to allow early identification (1 in 10,000 or less)

• Key Finding: Success - the cells can be isolated! • Next step: Assess gene expression (RNAseq) or mutations (WGA)

– Understand the heterogeneity at the single cell level by sorting single cells into 96-well plates

• Key implication: Identify early, potential targets for cancer therapy

Some sample data from the Chodosh lab, sorting DTCs from the bone marrow of a breast cancer patient with metastatic disease: Sorted 609 Her2/EpCAM

positive cells (in blue) from 6.7 million total events

Flow Cytometry & Cell Sorting Resource Laboratory

• Opportunity: a novel flow cytometer analyzer (the BD LSRFortessa X-50 – Beta test), using 5 lasers and up to 50 detectors, with novel electronics and software – Novel fluorescent probes are being identified – Involves sophisticated data analysis (the Initiative for Deep

Phenotyping) – Identify novel immune cells relevant to a wide variety of

diseases

CDB Microscopy Core

• Research Question: When is Hopx (an atypical homeodomain protein) first expressed during cardiogenesis? Prior to the expression and assembly of sarcomeres, defining structural components of cardiac myocytes?

• Method: Document Hopx and sarcomere gene expression during early time points - using CDB Microscopy resources –in combination with RNA-expression analysis

• Key Finding: Hopx is expressed prior to sarcomere genes

• Cover of Science, June 2015 Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts. Jain R, Li, D.… Epstein JA. Science. 2015.

Next Generation Sequencing Core • Research Question: Determine somatic sequence variants that might occur

in beta-cells of diabetic patients

• Method: Because beta-cells do not proliferate and form clones, this had to be done on the single cell level (sequenced 39 libraries to establish feasibility)

• Key Finding: Enabled determination of genomic locations of microdeletions that result from NHEJ (pathway that repairs double-strand breaks in DNA)

• figure shows a 16bp heterozygous deletion (black lines) found in a protein-coding exon which did not occur in any other cell that had coverage at this location

• Key Implication: Key data for $8M grant aimed at measuring the level of cellular damage on a single-cell level in old or T2D diabetic beta cells

Clinical Research Computing Unit • Research Question: Is Pharmacogenetic versus Clinical Algorithm dosing of

Warfarin more effective when initiating therapy? • Methods: Double Blind RCT- subjects randomized to either standard of

care (Clinical Algorithm dosing) or dosing based on genotype/clinical information for the first 5 days of therapy, followed for an additional 4 weeks

• Key Finding: Combining genetic data with clinical information to determine the initial dosage of the blood thinner warfarin was no more effective than using clinical information alone – In African-Americans, the genetics based approach had a slightly lower level of effectiveness

• Next Step: Understand the role genomics plays in determining optimal therapies

Transgenic and Chimeric Mouse Facility and Penn Gene Targeting Core

• Research Question: Is alternative splicing essential for posttranscriptional gene regulation, necessary for normal cellular function, patterning, and development

• Methods: Generated two conditional mouse knockout alleles, one complete knockout allele and a knockin mouse for two splicing factors discovered in Carstens lab (Esrp1 and Esrp2)

• Key Finding: Large scale programs for epithelial cell functions • Key Implication: Mouse models formed the core of two new NIH R01 grants • Publication “The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program

essential for mammalian development.”, eLife, September 2015

Outline • People and Cores • Recent Activities • Brief Summary of Each Core • Core Project Examples • Areas of Focus Going Forward

Key Areas of Focus

• Marketing / advertising of resources – General, new faculty, BGS, BPP – Website, workshops, symposia

• Annual reporting/core requests/surveys • Financial clarity • Aid in faculty recruiting

Key Areas of Focus (cont’d)

• iLAB trial and evaluation • Enhancement of core directors “community” • Departments vs PSOM “home” • Relationships/interactions with CHOP, Wistar, VA, etc

Outline • People and Cores • Recent Activities • Brief Summary of Each Core • Core Project Examples • Areas of Focus Going Forward